[Freesurfer] Questions about surface coordanates
Dear Experts, I tried to extract vertex coordinates information from 'fsaverage/surf/lh.pial' file using matlab function 'read_surf', but I found that the coordinates returned by the function are different from what I saw in tksurfer, here are the screenshots: The vertex index starts from 0 in tksurfer, so I select the second elements in matlab. Why is the result different from what has been shown in tksurfer(also different in freeview)? Which one should I report? Is there any way to transform the surface coordinates to the MNI152 space? Thank you very much! Dong ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] 答复: Questions about surface coordanates
Thanks a lot! Just want to make sure that the “RAS”(FS cords?) and “MNI Talairach” is the MNI305 coords. 发件人: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] 代表 Douglas Greve 发送时间: 2016年8月30日 21:21 收件人: freesurfer@nmr.mgh.harvard.edu 主题: Re: [Freesurfer] Questions about surface coordanates tksurfer always uses the ?h.orig coordinates. Also keep in mind that the vertex index is 0-based whereas matlab is 1-based. When you click on a point, you should see something like the following print out selected vertex 123491 out of 163842 current -39.11 15.65 11.26 orig -55.67 -10.37 19.95 pial 0.00 0.00 0.00 white-55.76 -10.29 19.93 On 8/30/16 5:12 AM, Dongnandi wrote: Dear Experts, I tried to extract vertex coordinates information from ‘fsaverage/surf/lh.pial’ file using matlab function ‘read_surf’, but I found that the coordinates returned by the function are different from what I saw in tksurfer, here are the screenshots: The vertex index starts from 0 in tksurfer, so I select the second elements in matlab. Why is the result different from what has been shown in tksurfer(also different in freeview)? Which one should I report? Is there any way to transform the surface coordinates to the MNI152 space? Thank you very much! Dong ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Longitudinal proceesing for Pediatric data
Dear freesurfer exports, As it is mentioned in the documentation that 'pediatric data violates the fixed head size assumption' for the current longitudinal stream. Is there any solution for the issue now? Thanks Dong ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] 答复: Longitudinal proceesing for Pediatric data
Hi Martin Thanks a lot for your reply! Is there any reference that the longitudinal processing would fail if the difference in head size exceeded any certain value? Best, Dong 发件人: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] 代表 Martin Reuter 发送时间: 2017年2月15日 2:40 收件人: Freesurfer support list 主题: Re: [Freesurfer] Longitudinal proceesing for Pediatric data Hi Dong, it can work, if time points are close to each other (so not much head growth). Feel free to try, but make sure you are carefully looking at the surfaces, that no gray matter is clipped in later time points. The alternative is to only do cross sectional processing. Best, Martin On 14 Feb 2017, at 04:56, Dongnandi mailto:dongnan...@163.com> > wrote: Dear freesurfer exports, As it is mentioned in the documentation that ‘pediatric data violates the fixed head size assumption’ for the current longitudinal stream. Is there any solution for the issue now? Thanks Dong ___ Freesurfer mailing list <mailto:Freesurfer@nmr.mgh.harvard.edu> Freesurfer@nmr.mgh.harvard.edu <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] fs6.0 mri_surf2surf failure
Dear FS experts,
I'm trying to transform some files from fsaverage space to
fsaverage5 space using mri_surf2surf(fs version: 6.0), however, it is weird
that the results turn out to be all zeros on the fsaverage5 surface, the
command line I used if : mri_surf2surf -srcsubject fsaverage -sval
${hemi}.fsaverage.nii.gz -hemi ${hemi} --cortex -trgsubject fsaverage5
-tval ${hemi}.fsaverage5.nii.gz -surfreg sphere.reg. There is no error
reported.
The strange thing is that it works well using FS5.3, it failed
after I update to FS 6.0. Any suggestion of solving this?
Many thanks!
Best!
Dong
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[Freesurfer] mri_surf2surf failure in FS6.0
Dear Freesurfer experts, I have a binary brainmask made in volumetric space and trying to transfer it into surface space, first I use mri_vol2surf to transfer the mask into fsaverage space, then run mri_surf2surf (fs 6.0) to down sample it to fsaverage5 space. After vol2surf, some values on the vertex in fsaverage space would be less than 1 due to the interpolation, however, I find values on these vertexes (<1 in fsaverage) come to be 0 after mri_surf2surf in faverage5 space. it doesn't happen in version 5.3, how can I solve this in 6.0? Many thanks, Dong Haoming ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
